Cooperativity flows and shear-bandings: a statistical field theory approach.

Cooperativity effects have been proposed to explain the non-local rheology in the dynamics of soft jammed systems. Based on the analysis of the free-energy model proposed by L. Bocquet, A. Colin and A. Ajdari, Phys. Rev. Lett., 2009, 103, 036001, we show that cooperativity effects resulting from the non-local nature of the fluidity (inverse viscosity) are intimately related to the emergence of shear-banding configurations. This connection materializes through the onset of inhomogeneous compact solutions (compactons), wherein the fluidity is confined to finite-support subregions of the flow and strictly zero elsewhere. The compacton coexistence with regions of zero fluidity ("non-flowing vacuum") is shown to be stabilized by the presence of mechanical noise, which ultimately shapes up the equilibrium distribution of the fluidity field, the latter acting as an order parameter for the flow-noflow transitions occurring in the material.

Internal dynamics and activated processes in soft-glassy materials.

Plastic rearrangements play a crucial role in the characterization of soft-glassy materials, such as emulsions and foams. Based on numerical simulations of soft-glassy systems, we study the dynamics of plastic rearrangements at the hydrodynamic scales where thermal fluctuations can be neglected. Plastic rearrangements require an energy input, which can be either provided by external sources, or made available through time evolution in the coarsening dynamics, in which the total interfacial area decreases as a consequence of the slow evolution of the dispersed phase from smaller to large droplets/bubbles. We first demonstrate that our hydrodynamic model can quantitatively reproduce such coarsening dynamics. Then, considering periodically oscillating strains, we characterize the number of plastic rearrangements as a function of the external energy-supply, and show that they can be regarded as activated processes induced by a suitable "noise" effect. Here we use the word noise in a broad sense, referring to the internal non-equilibrium dynamics triggered by spatial random heterogeneities and coarsening. Finally, by exploring the interplay between the internal characteristic time-scale of the coarsening dynamics and the external time-scale associated with the imposed oscillating strain, we show that the system exhibits the phenomenon of stochastic resonance, thereby providing further credit to the mechanical activation scenario.

Direct evidence of plastic events and dynamic heterogeneities in soft-glasses.

By using fluid-kinetic simulations of confined and concentrated emulsion droplets, we investigate the nature of space non-homogeneity in soft-glassy dynamics and provide quantitative measurements of the statistical features of plastic events in the proximity of the yield-stress threshold. Above the yield stress, our results show the existence of a finite stress correlation scale, which can be mapped directly onto the cooperativity scale, recently introduced in the literature to capture non-local effects in the soft-glassy dynamics. In this regime, the emergence of a separate boundary (wall) rheology with higher fluidity than the bulk is highlighted in terms of near-wall spontaneous segregation of plastic events. Near the yield stress, where the cooperativity scale cannot be estimated with sufficient accuracy, the system shows a clear increase of the stress correlation scale, whereas plastic events exhibit intermittent clustering in time, with no preferential spatial location. A quantitative measurement of the space-time correlation associated with the motion of the interface of the droplets is key to spot the elastic rigidity of the system.

Heterogeneous diffuse interfaces: a new mechanism for arrested coarsening in binary mixtures. Heterogeneous diffuse interfaces.

We discuss the dynamics of binary fluid mixtures in which surface tension density is allowed to become locally negative within the interface, while still preserving positivity of the overall surface tension (heterogeneous diffuse interface). Numerical simulations of two-dimensional Ginzburg-Landau phase field equations implementing such mechanism and including hydrodynamic motion, show evidence of dynamically arrested domain coarsening. Under specific conditions on the functional form of the surface tension density, dynamical arrest can be interpreted in terms of the collective dynamics of metastable, non-linear excitations of the density field, named compactons, as they are localized to finite-size regions of configuration space and strictly zero elsewhere. Aside from compactons, the heterogeneous diffuse interface scenario appears to provide a robust mechanism for the interpretation of many aspects of soft-glassy behaviour in binary fluid mixtures.

Phase-field model of long-time glasslike relaxation in binary fluid mixtures.

We present a new phase-field model for binary fluids, exhibiting typical signatures of soft-glassy behavior, such as long-time relaxation, aging, and long-term dynamical arrest. The present model allows the cost of building an interface to vanish locally within the interface, while preserving positivity of the overall surface tension. A crucial consequence of this property, which we prove analytically, is the emergence of free-energy minimizing density configurations, hereafter named "compactons," to denote their property of being localized to a finite-size region of space and strictly zero elsewhere (no tails). Thanks to compactness, any arbitrary superposition of compactons still is a free-energy minimizer, which provides a direct link between the complexity of the free-energy landscape and the morphological complexity of configurational space.

Three-band decomposition analysis of wall shear stress in pulsatile flows.

Space-time patterns of wall shear stress (WSS) resulting from the numerical simulation of pulsating hemodynamic flows in semicoronal domains are analyzed, in the case of both regular semicoronal domains and semicoronal domains with bumpy insertions, mimicking aneurysm-like geometries. A new family of cardiovascular risk indicators, which we name three-band diagrams (TBDs), are introduced, as a sensible generalization of the two standard indicators, i.e., the time-averaged WSS and the oscillatory shear index. TBDs provide a handy access to additional information contained in the dynamic structure of the WSS signal as a function of the physiological risk threshold, thereby allowing a quick visual assessment of the risk sensitivity to individual fluctuations of the physiological risk thresholds. Due to its generality, TBD analysis is expected to prove useful for a wide host of applications in science, engineering, and medicine, where risk assessment plays a central role.

Optimization of HAART with genetic algorithms and agent-based models of HIV infection.

MOTIVATION: Highly Active AntiRetroviral Therapies (HAART) can prolong life significantly to people infected by HIV since, although unable to eradicate the virus, they are quite effective in maintaining control of the infection. However, since HAART have several undesirable side effects, it is considered useful to suspend the therapy according to a suitable schedule of Structured Therapeutic Interruptions (STI). In the present article we describe an application of genetic algorithms (GA) aimed at finding the optimal schedule for a HAART simulated with an agent-based model (ABM) of the immune system that reproduces the most significant features of the response of an organism to the HIV-1 infection. RESULTS: The genetic algorithm helps in finding an optimal therapeutic schedule that maximizes immune restoration, minimizes the viral count and, through appropriate interruptions of the therapy, minimizes the dose of drug administered to the simulated patient. To validate the efficacy of the therapy that the genetic algorithm indicates as optimal, we ran simulations of opportunistic diseases and found that the selected therapy shows the best survival curve among the different simulated control groups. AVAILABILITY: A version of the C-ImmSim simulator is available at http://www.iac.cnr.it/~filippo/c-ImmSim.html

An enhanced agent based model of the immune system response.

We describe some recent enhancements introduced in C-ImmSim, a simulator of the immune system response that we have been developing for a number of years along with preliminary results produced by the simulation of the Highly Active Anti-Retroviral Therapy in HIV-1 infected patients.

Intracellular signal propagation in a two-dimensional autocatalytic reaction model.

We study a simple reaction scheme in a two-dimensional lattice of particles or molecules with a refractory state. We analyze the dynamics of the propagating front as a function of physical-chemical properties of the host medium. The anisotropy of the medium significantly affects the smoothness of the wave front. Similarly, if particles or molecules may diffuse slowly to neighboring sites, then the front wave is more likely to be irregular. Both situations affect the ability of the whole system to relax to the original state, which is a required feature in the biological cells. Attempts to map this simple reaction scheme to reactions involved in the intracellular pathways suggest that, in some cases, signal transduction might take both connotation of a random walk and a propagating wave, depending on the local density of the medium. In particular, a sufficient condition for the appearance of waves in high-density regions of the media, is the existence of at least one autocatalytic reaction in the chain of reactions characterizing the pathway.

Selection of escape mutants from immune recognition during HIV infection.

We present computer simulations of the HIV infection based ona sophisticated cellular automata model of the immune response. The infection progresses following the well-known three-phase dynamics observed in patients, that is, acute, silent and acquired immunodeficiency.Antigenic shift and selection of escape viral mutants with low transcription rate explain the long term course of the asymptomatic phase, while the immunodeficiency status appears to be the consequence of a drastic reduction in T helper cell repertoire.

Design and implementation of an immune system simulator.

Cellular automata based models have proven capable of providing several new insights into the dynamics of the immune system (IS) response.A qualitative picture of the IS behavior can be obtained with small-scale simulations. However, for a more detailed analysis and to further validate the models, large-scale simulations are required. To this purpose we present here a simulator (PARIMM) of the IS response which has been carefully designed and coded to allow such simulations (millions of cells with a very high degree of complexity). The code does not just resort to parallel processing to run faster. Data structures and I/O have been optimized as well to limit the (huge) memory and disk space requirements. The recent addition of the description of the T killer cellular mediated response allows the code to simulate both humoral and cellular immune reactions. All these features put PARIMM among the most complete simulators of the immune system developed up today.

Large-scale cellular automata simulations of the immune system response.

The sequential nature of the process allowing the immune system to learn how to withstand pathogen agents is explored by means of large-scale computer simulation of the Celada-Seiden immunological automaton. In accord with our previous results, it is found that the learning process proceeds via a sequential cascade in affinity space.